Tutorial for R Markdown and R Notebook

This presentation gives a brief introduction to R Markdown and R Notebooks and this tutorial is adapted from introductory materials on their websites.

Overview

R Markdown is a text file type that has the extension .Rmd.

It provides a reproducible document framework for data science, and you can use a single R Markdown file to both

• save and execute codes
• generate high quality reports that can be shared with an audience

When you open the R Markdown file in the RStudio IDE, it becomes an R Notebook interface.

R Notebook is an R Markdown document with chunks that can be executed independently and interactively. Any R Markdown document can be used as a notebook, and all R Notebooks can be rendered to other R Markdown document types. A notebook can therefore be thought of as a special execution mode for R Markdown documents.

Creating an R Notebook

You can create a new notebook in RStudio with the menu command File -> New File -> R Notebook, or by using the html_notebook output type in your document’s YAML header.

After that, you will have an R Notebook with one code chunk.

Markdown Basics

Format the text in your R Markdown file with Pandoc’s Markdown, a set of markup annotations for plain text files. When you render your file, Pandoc transforms the marked up text into formatted text in your final file format:

Inserting Chunks

In each chunk, the codes can be executed independently, and the output will appear beneath the chunk.

New chunks can be inserted quickly using the keyboard shortcut Ctrl + Alt + I (OS X: Cmd + Option + I), or via the Add Chunk command in the editor toolbar.

Chunk Options

Chunk output can be customized with knitr options, arguments set in the {} of a chunk header. Above, we use five arguments:

• include = FALSE prevents code and results from appearing in the finished file. R Markdown still runs the code in the chunk, and the results can be used by other chunks.
• echo = FALSE prevents code, but not the results from appearing in the finished file. This is a useful way to embed figures.
• message = FALSE prevents messages that are generated by code from appearing in the finished file.
• warning = FALSE prevents warnings that are generated by code from appearing in the finished.
• fig.cap = "..." adds a caption to graphical results.

Also, you can process many languages in code chunks besides R. Some of the available language engines include:

• Python
• SQL
• Bash
• Stan
• JavaScript

To process a code chunk using an alternate language engine, replace the r at the start of your chunk declaration with the name of the language:

Saving Your R Notebook

When you finish your R Notebook, you can choose to save the .Rmd file. At the same time, an .nb.html file is created alongside it. This file is a self-contained HTML file which contains both a rendered copy of the notebook with all current chunk outputs (suitable for display on a website) and a copy of the notebook .Rmd itself.

Also, the RStudio IDE knit button allows you to render your R Notebook to other formats like .pdf and .docx. You can render to additional formats by clicking the dropdown menu beside the knit button:

Here is how it works:

References

1. R Markdown from R Studio http://rmarkdown.rstudio.com/lesson-1.html

2. R Notebook from R Studio http://rmarkdown.rstudio.com/r_notebooks.html